I just uploaded a fix. This should be corrected in version 1.9.14
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Robert Castelo
<robert.cast...@upf.edu>
Sent: Wednesday, October 5, 2016 1:00:21 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()
hi,
there's a warning issued by GenomeInfoDb::keepStandardChromosomes()
because of multiple compatible sequence styles, that i guess it should
be corrected. this warning can be reproduced minimally as follows;
library(GenomicRanges)
library(GenomeInfoDb)
gr <- GRanges(seqnames="1", IRanges(1, 10))
gr <- keepStandardChromosomes(gr)
Warning message:
In if (!is.na(guess)) style <- unique(guess$style) else
return(dropSeqlevels(x, :
the condition has length > 1 and only the first element will be used
you can find the session info below. the specific line of code affected
on the lastest SVN version of GenomeInfoDb is:
keepStandardChromosomes <- function(x, species=NULL)
{
ori_seqlevels <- seqlevels(x)
if(!length(ori_seqlevels))
return(x)
## guess at style
guess <- .guessSpeciesStyle(ori_seqlevels)
if (!is.na(guess))
style <- unique(guess$style)
[...]
cheers,
robert.
ps: sessionInfo()
R Under development (unstable) (2016-05-04 r70581)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices
[6] utils datasets methods base
other attached packages:
[1] GenomicRanges_1.25.94 GenomeInfoDb_1.9.13
[3] IRanges_2.7.16 S4Vectors_0.11.17
[5] BiocGenerics_0.19.2 setwidth_1.0-4
[7] colorout_1.0-3
loaded via a namespace (and not attached):
[1] zlibbioc_1.19.0 XVector_0.13.7
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
